EBNA1BP2

protein-coding

EBNA1 binding protein 2, the group of MicroRNA protein coding host genes

Gene summary

Enables RNA binding activity. Predicted to be involved in rRNA processing and ribosomal large subunit biogenesis. Located in chromosome and nucleolus. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_006824.3

Inheritance

—

ClinVar variants

U:39B:3

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.73

Max pathogenic AF

—

Genomic locus

chr1:43,164,175-43,270,936

External References & Databases

Ensembl (ENSG00000117395)

Transcript & Mutation Effects

hg38 • Region Span ~106.8 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to EBNA1BP2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 32

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_006824.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			36 clinvar	1 clinvar	2 clinvar	39
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	39	1	2	42

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 11 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_006824.3	RefSeq	NP_006815.2	9	MANE Select
ENST00000236051.3	Ensembl	ENSP00000236051.2	9	MANE Select
NM_001159936.1	RefSeq	NP_001153408.1	10	Standard
ENST00000431635.6	Ensembl	ENSP00000407323.2	10	Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / Model	Organism	Observed Phenotype
ebna1bp2	Danio rerio	Structure: pigment cell Quality: quality abnormal

Gene / Model

Organism

Observed Phenotype

ebna1bp2

Danio rerio

Structure: pigment cell

Quality: quality

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

rRNA processing
ribosomal large subunit biogenesis

Molecular Function

RNA binding

Cellular Component

nucleus
nucleolus
preribosome, large subunit precursor
nuclear periphery

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000431635
Coding exons: 10
Length: 106762
Individuals with no LoFs: 125557
Homozygous LoFs: 0
Heterozygous LoFs: 191
Defined: 125748
p: 0.000760

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.266	200	211	0.948	0.0000109	2361
Missense (PolyPhen)		32	46.176	0.693		557
Synonymous	0.273	77	80.1	0.961	0.00000426	680
Loss of Function	1.23	17	23.4	0.726	0.00000137	237

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00032	0.00031	rare
Latino/Admixed American	0.0033	0.0033	notable
Ashkenazi Jewish	0	0.0	absent
East Asian	0.0015	0.0015	notable
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00015	0.00015	rare
South Asian	0.00085	0.00085	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Required for the processing of the 27S pre-rRNA. {ECO:0000250}.;

Recessive Scores

pRec: 0.127

Intolerance Scores

LoFtool: 0.942
RVIS EVS: 0.42
RVIS percentile EVS: 76.96

Essentials

Essential (CRISPR): E
Essential (CRISPR2): E
Essential (gene trap): E
Indispensability pred.: E
Indispensability score: 0.895

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium